debian/0000755000000000000000000000000012175413724007174 5ustar debian/source/0000755000000000000000000000000012175413233010467 5ustar debian/source/format0000644000000000000000000000001412175413233011675 0ustar 3.0 (quilt) debian/copyright0000644000000000000000000003337712175406334011143 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Source: http://search.cpan.org/CPAN/authors/id/L/LD/LDS/Bio-Graphics-2.33.tar.gz Comment: On Debian systems, copies of the GNU General Public License version 1 and Lesser General Public License version 2.1 can be found respectively in ‘/usr/share/common-licenses/GPL-1’ and ‘/usr/share/common-licenses/LGPL-2.1’. License: perl-and-more Most files in this package are distributed under the same terms as Perl itself, but there are also a few files under ‘LGPL-2.1+ or Artistic-2.0’ or ‘GPL-1+ or Artistic-2.0’, which are compatible. Files: * Copyright: 2001-2010, Cold Spring Harbor Laboratory License: Perl Comment: This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See the Artistic License file in the main Perl distribution for specific terms and conditions of use. In addition, the following disclaimers apply: . CSHL makes no representations whatsoever as to the SOFTWARE contained herein. It is experimental in nature and is provided WITHOUT WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE OR ANY OTHER WARRANTY, EXPRESS OR IMPLIED. CSHL MAKES NO REPRESENTATION OR WARRANTY THAT THE USE OF THIS SOFTWARE WILL NOT INFRINGE ANY PATENT OR OTHER PROPRIETARY RIGHT. . By downloading this SOFTWARE, your Institution hereby indemnifies CSHL against any loss, claim, damage or liability, of whatsoever kind or nature, which may arise from your Institution's respective use, handling or storage of the SOFTWARE. . If publications result from research using this SOFTWARE, we ask that CSHL be acknowledged and/or credit be given to CSHL scientists, as scientifically appropriate. Files: lib/Bio/Graphics/Glyph/rndrect.pm lib/Bio/Graphics/Glyph/splice_site.pm lib/Bio/Graphics/Glyph/extending_arrow.pm Copyright: © 2001 Berkeley Drosophila Genome Project License: Perl Files: lib/Bio/Graphics/Pictogram.pm Copyright: © Shawn Hoon License: Perl Files: lib/Bio/Graphics/RendererI.pm Copyright: © 2003 Institute for Systems Biology License: Perl Files: lib/Bio/Graphics/ConfiguratorI.pm Copyright: © Robert Hubley License: Perl Files: lib/Bio/Graphics/Glyph/hybrid_plot.pm lib/Bio/Graphics/Glyph/scale.pm Copyright: © 2008,2010 Ontario Institute for Cancer Research License: Perl Files: lib/Bio/Graphics/Glyph/allele_tower.pm Copyright: © 2003 Cold Spring Harbor Laboratory License: GPL-1+ or Artistic-2.0 Author: Fiona Cunningham in Lincoln Stein's lab Files: lib/Bio/Graphics/FeatureDir.pm lib/Bio/Graphics/Glyph/pairplot.pm lib/Bio/Graphics/Glyph/generic.pm Copyright: 2008,2009,2010 Ontario Institute for Cancer Research 2001,2004 Cold Spring Harbor Laboratory License: GPL-1+ or Artistic-2.0 Files: lib/Bio/Graphics/Layout.pm Copyright: © 2007-2010 The Evolutionary Software Foundation License: LGPL-2.1+ or Artistic-2.0 License: Artistic-2.0 Copyright (c) 2000-2006, The Perl Foundation. . 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License: GPL-1+ This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 1, or (at your option) any later version. . This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston MA 02110-1301 USA Comment: On Debian systems, the complete text of the GNU General Public License version 1 can be found in ‘/usr/share/common-licenses/GPL-1’. License: LGPL-2.1+ This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. . This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. . You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA Comment: On Debian systems, the complete text of the GNU Lesser General Public License version 2.1 can be found in ‘/usr/share/common-licenses/LGPL-2.1’. License: Perl This program is free software; you can redistribute it and/or modify it under the terms of either: . a) the GNU General Public License as published by the Free Software Foundation; either version 1, or (at your option) any later version, or . b) the "Artistic License" which comes with Perl. Comment: On Debian systems, the complete text of the Artistic License can be found in ‘/usr/share/common-licenses/Artistic’, and the complete text of the latest version of the GNU General Public License version 1 can be found in ‘/usr/share/common-licenses/GPL-1’. debian/gbp.conf0000644000000000000000000000032112175406334010606 0ustar # This source package is managed with git-buildpackage and pristine-tar. [DEFAULT] # use pristine-tar: pristine-tar = True [git-dch] # include 7 digits of the commit id in the changelog entry: id-length = 7 debian/compat0000644000000000000000000000000212175406334010371 0ustar 9 debian/watch0000644000000000000000000000035512175406334010227 0ustar # format version number, currently 3; this line is compulsory! version=3 # URL to the package page followed by a regex to search http://search.cpan.org/dist/Bio-Graphics/ .*/Bio-Graphics-v?(\d[\d_.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz|zip)$ debian/examples0000644000000000000000000000000512175406334010727 0ustar eg/* debian/docs0000644000000000000000000000003212175406334010041 0ustar README debian/README.test debian/patches/0000755000000000000000000000000012175413112010612 5ustar debian/patches/skip_image_tests0000644000000000000000000000072712175413112014075 0ustar Subject: ignore image tests causing test errors Description: Image tests creates some error preventing build. Forwarded: yes Bug: https://rt.cpan.org/Ticket/Display.html?id=87391 Author: Olivier Sallou Last-Updated: 2013-07-29 --- a/t/BioGraphics.t +++ b/t/BioGraphics.t @@ -15,7 +15,7 @@ # for now, the image tests are turned off use lib "$Bin/../lib"; -use constant IMAGE_TESTS => 1; +use constant IMAGE_TESTS => 0; BEGIN { use lib '.'; debian/patches/series0000644000000000000000000000002112175413016012023 0ustar skip_image_tests debian/control0000644000000000000000000000261112175406334010576 0ustar Source: libbio-graphics-perl Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Olivier Sallou Section: perl Priority: optional Build-Depends: debhelper (>= 9), perl # Needed for the tests Build-Depends-Indep: bioperl (>= 1.6.0), libgd-gd2-perl (>= 2.3), libstatistics-descriptive-perl Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/libbio-graphics-perl.git Vcs-Git: git://anonscm.debian.org/debian-med/libbio-graphics-perl.git Homepage: http://search.cpan.org/dist/Bio-Graphics/ Package: libbio-graphics-perl Architecture: all Depends: ${perl:Depends}, ${misc:Depends}, bioperl, libgd-gd2-perl Recommends: libbio-scf-perl, perl, libgd-svg-perl, libstatistics-descriptive-perl Description: Generate GD images of Bio::Seq objects The Bio::Graphics::Panel class provides drawing and formatting services for any object that implements the Bio::SeqFeatureI interface, including Ace::Sequence::Feature, Das::Segment::Feature and Bio::DB::Graphics objects. It can be used to draw sequence annotations, physical (contig) maps, protein domains, or any other type of map in which a set of discrete ranges need to be laid out on the number line. debian/rules0000755000000000000000000000013412175406334010251 0ustar #!/usr/bin/make -f %: dh $@ override_dh_installchangelogs: dh_installchangelogs Changes debian/README.test0000644000000000000000000000076412175406334011040 0ustar Notes on how this package is tested. ──────────────────────────────────── The maintainer relies on the package's regression tests that are executed at build time on his computer. The build logs are stored in a Git repository and can be browsed on line. http://git.debian.org/?p=debian-med/libbio-graphics-perl.git;a=blob;hb=refs/heads/meta;f=amd64.log -- Charles Plessy Thu, 14 Jul 2011 19:26:44 +0900 debian/upstream0000644000000000000000000000037312175406334010761 0ustar Archive: CPAN Contact: Lincoln Stein Homepage: http://search.cpan.org/dist/Bio-Graphics/ Name: Bio::Graphics Watch: http://search.cpan.org/dist/Bio-Graphics/ .*/Bio-Graphics-v?(\d[\d_.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz|zip)$ debian/changelog0000644000000000000000000001640712175413637011061 0ustar libbio-graphics-perl (2.37-1) unstable; urgency=low * New upstream release 2.37 * Remove failing tests (Closes: #718147). -- Olivier Sallou Mon, 29 Jul 2013 08:42:51 +0200 libbio-graphics-perl (2.33-1) unstable; urgency=low befc3bc Imported Upstream version 2.33 68d9d7b Removed obsolete DM-Upload-Allowed field. 3c16457 Normalised Debian control and copyright files with config-model-edit. 2e26637 Removed obsolete Breaks statement. bdf87e1 Using Debhelper 9. d06499c Normalised VCS URLs following Lintian's standard. 72c9b22 Conforms to Policy 3.9.4. -- Charles Plessy Sun, 05 May 2013 22:29:14 +0900 libbio-graphics-perl (2.32-1) unstable; urgency=low 63f795d New upstream release 2.32 -- Olivier Sallou Sat, 15 Dec 2012 11:20:43 +0100 libbio-graphics-perl (2.31-1) unstable; urgency=low e5dd936 New upstream release 2.31 -- Olivier Sallou Sat, 15 Dec 2012 10:00:47 +0100 libbio-graphics-perl (2.29-1) unstable; urgency=low 5f027b7 Imported Upstream version 2.29. bdb8255 Summarised license for the whole package with a header field. 9ce13ce Conforms to Debian Policy version 3.9.3. -- Charles Plessy Sun, 09 Sep 2012 12:18:11 +0900 libbio-graphics-perl (2.26-1) unstable; urgency=low * New upstream release (Closes: #660481). -- Charles Plessy Mon, 20 Feb 2012 13:05:39 +0900 libbio-graphics-perl (2.24-1) unstable; urgency=low * New usptream release. * Replaced deprecated ‘<’ by ‘<<’ in debian/control. * Renamed debian/README.Debian debian/README.test, as it only discusses tests * Incremented Standards-Version to reflect conformance with Policy 3.9.1 (debian/control, no changes needed). -- Charles Plessy Thu, 14 Jul 2011 19:50:40 +0900 libbio-graphics-perl (2.14-1) unstable; urgency=low * New upstream release. * Converted debian/copyright to DEP-5 machine-readable format. * Incremented Standards-Version to reflect conformance with Policy 3.9.1 (debian/control, no changes needed). * Source package now managed with Git (debian/control). * Using Debhelper 8 (debian/control, debian/compat). -- Charles Plessy Wed, 23 Mar 2011 15:45:48 +0900 libbio-graphics-perl (2.11-1) unstable; urgency=low * New upstream release. * Conformance with Policy 3.9.0: - Use Breaks instead of Conflicts (debian/control). - Incremented Standards-Version to reflect conformance (debian/control). * Mention the download directory instead of the full URL as Source in debian/copyright. -- Charles Plessy Tue, 13 Jul 2010 10:39:44 +0900 libbio-graphics-perl (2.10-1) unstable; urgency=low * New upstream release. * Using Debhelper's ‘dh’ (debian/rules, debian/docs, debian/examples). * Recommends libfile-spec-perl (debian/control). -- Charles Plessy Fri, 25 Jun 2010 20:02:53 +0900 libbio-graphics-perl (2.02-1) unstable; urgency=low * New upstream release (more support for BigWig and BigBed data, and other changes). * Build-depend on libstatistics-descriptive-perl, needed for the tests. * Recommend libbio-scf-perl, libgd-svg-perl, libstatistics-descriptive-perl, according to META.yaml. * Added a few words in debian/README.Debian on how this package is tested. -- Charles Plessy Mon, 29 Mar 2010 22:23:43 +0900 libbio-graphics-perl (2.01-1) unstable; urgency=low * New upstream release. -- Charles Plessy Sat, 06 Mar 2010 19:21:41 +0900 libbio-graphics-perl (2.00-1) unstable; urgency=low * New upstream release. * Incremented Standards-Version to reflect conformance with Policy 3.8.4 (debian/control, no other changes needed). -- Charles Plessy Thu, 11 Feb 2010 22:45:02 +0900 libbio-graphics-perl (1.995-1) unstable; urgency=low * New upstream release. -- Charles Plessy Fri, 08 Jan 2010 13:27:40 +0900 libbio-graphics-perl (1.994-1) unstable; urgency=low * New upstream releases. * debian/copyright: - Updated for new upstream file. - Added Artistic license version 2.0. -- Charles Plessy Fri, 11 Dec 2009 13:42:21 +0900 libbio-graphics-perl (1.992-1) unstable; urgency=low * New upstream release. * Added a couple of informations in debian/upstream-metadata.yaml. -- Charles Plessy Sun, 22 Nov 2009 22:33:46 +0900 libbio-graphics-perl (1.982-1) unstable; urgency=low * New upstream release fixing DAS stylesheet support. * Enhances: gbrowse (debian/control). -- Charles Plessy Fri, 02 Oct 2009 21:07:17 +0900 libbio-graphics-perl (1.981-1) unstable; urgency=low * New upstream release fixing bugs in wiggle_xyplot and improving documentation. * debian/control: incremented Standards-Version to reflect conformance with Policy 3.8.3 (no changes needed). * Removed trailing spaces in debian/changelog. -- Charles Plessy Mon, 24 Aug 2009 12:53:39 +0900 libbio-graphics-perl (1.97-1) unstable; urgency=low * New upstream release adding a “feature_limit” option. * debian/control: incremented Standards-Version to reflect conformance with Policy 3.8.2 (no changes needed). * Format experimentations on debian/copyright. -- Charles Plessy Fri, 10 Jul 2009 19:12:27 +0900 libbio-graphics-perl (1.96-1) unstable; urgency=low * New upstream release improving DAS 1.5 support. * Documented in debian/copyright files distributed under the GPL version 1 or superior, or the Artistic license version 2. Ignored VCS leftovers ‘lib/Bio/Graphics/Glyph/.#dna.pm.1.1’ and ‘lib/Bio/Graphics/Glyph/.#hybrid_plot.pm.1.2’. -- Charles Plessy Wed, 10 Jun 2009 13:04:42 +0900 libbio-graphics-perl (1.95-1) unstable; urgency=low * New upstream release, improving SVG support. -- Charles Plessy Thu, 04 Jun 2009 19:05:06 +0900 libbio-graphics-perl (1.94-1) unstable; urgency=low * New upstream release, adding a “fast” option and fixing error in xyplot. -- Charles Plessy Sun, 03 May 2009 18:24:13 +0900 libbio-graphics-perl (1.93-1) unstable; urgency=low * New upstream release (corrections and improved documentation). * debian/copyright made simpler according to current discussion on machine-readable format. -- Charles Plessy Thu, 09 Apr 2009 10:40:38 +0900 libbio-graphics-perl (1.91-1) unstable; urgency=low * New upstream release with improvements on wiggle xyplots. * debian/control: checked conformance with Policy 3.8.1. -- Charles Plessy Fri, 20 Mar 2009 18:49:47 +0900 libbio-graphics-perl (1.85-1) unstable; urgency=low * New upstream release: - Adds including capacities in the configuration files. - New object: Bio::Graphics::Glyph::hybrid_plot. * debian/copyright: incremented year and added new holder. * debian/rules: replaced deprecated `dh_clean -k' by `dh_prep'. -- Charles Plessy Wed, 11 Mar 2009 10:23:12 +0900 libbio-graphics-perl (1.84-1) unstable; urgency=low * Initial Release. (Closes: #511382) -- Charles Plessy Sat, 10 Jan 2009 17:49:21 +0900